Error about mutation_zeroshot.py #95
Description
When I run python command like this : python mutation_zeroshot.py -c SaProt/config/ClinVar/saprot.yaml , the error happens. The information is listed below:
data/Users/zengbing1/software/anaconda3/envs/esm/lib/python3.11/site-packages/torchmetrics/utilities/prints.py:43: UserWarning: Metric SpearmanCorrcoef will save all targets and predictions in the buffer. For large datasets, this may lead to large memory footprint.
warnings.warn(*args, **kwargs) # noqa: B028
GPU available: True (cuda), used: True
TPU available: False, using: 0 TPU cores
IPU available: False, using: 0 IPUs
HPU available: False, using: 0 HPUs
0%| | 0/2525 [00:00<?, ?it/s]NP_891847.1.csv
0%| | 0/2525 [00:00<?, ?it/s]
Traceback (most recent call last):
File "/data3/soft/User/zengbing/method_data3/PLM/SaProt/scripts/mutation_zeroshot.py", line 71, in
main()
File "/data3/soft/User/zengbing/method_data3/PLM/SaProt/scripts/mutation_zeroshot.py", line 66, in main
run(config)
File "/data3/soft/User/zengbing/method_data3/PLM/SaProt/scripts/mutation_zeroshot.py", line 41, in run
result = trainer.test(model=model, datamodule=data_module)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/data/Users/zengbing1/software/anaconda3/envs/esm/lib/python3.11/site-packages/pytorch_lightning/trainer/trainer.py", line 755, in test
return call._call_and_handle_interrupt(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/data/Users/zengbing1/software/anaconda3/envs/esm/lib/python3.11/site-packages/pytorch_lightning/trainer/call.py", line 43, in _call_and_handle_interrupt
return trainer.strategy.launcher.launch(trainer_fn, *args, trainer=trainer, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/data/Users/zengbing1/software/anaconda3/envs/esm/lib/python3.11/site-packages/pytorch_lightning/strategies/launchers/subprocess_script.py", line 102, in launch
return function(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/data/Users/zengbing1/software/anaconda3/envs/esm/lib/python3.11/site-packages/pytorch_lightning/trainer/trainer.py", line 795, in _test_impl
results = self._run(model, ckpt_path=ckpt_path)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/data/Users/zengbing1/software/anaconda3/envs/esm/lib/python3.11/site-packages/pytorch_lightning/trainer/trainer.py", line 938, in _run
_verify_loop_configurations(self)
File "/data/Users/zengbing1/software/anaconda3/envs/esm/lib/python3.11/site-packages/pytorch_lightning/trainer/configuration_validator.py", line 42, in _verify_loop_configurations
__verify_eval_loop_configuration(model, "test")
File "/data/Users/zengbing1/software/anaconda3/envs/esm/lib/python3.11/site-packages/pytorch_lightning/trainer/configuration_validator.py", line 115, in __verify_eval_loop_configuration
raise NotImplementedError(
NotImplementedError: Support for test_epoch_end has been removed in v2.0.0. SaprotFoldseekMutationModel implements this method. You can use the on_test_epoch_end hook instead. To access outputs, save them in-memory as instance attributes. You can find migration examples in Lightning-AI/pytorch-lightning#16520. Can you help me? Many thanks.